NEWS.md

In compbiomed/TBSignatureProfiler: Profile RNA-Seq Data Using TB Pathway Signatures

TBSignatureProfiler 1.17.0

TBSignatureProfiler 1.16.0

Bug Fixes

• Removed references to compbiomed repository and replaced with wejlab.
• Fixed calls to GSVA package dependency to reflect new implementation (runTBsigProfiler)
• Updated vignette to reflect more recent results (using more signatures than when package was first released)

TBSignatureProfiler 1.14.0

Bug Fixes

• Fixed bug for signatureBoxplot by removing quotations around variables. This issue was introduced with the newest ggplot2 version. Thanks to Arthur VanValkenburg for identifying the issue and solution.
• Removed Zimmer_RES_3 which was an identical signature as the previously published Sweeney_OD_3.
• Fixed error in example for compare_algs caused by the signature being used.

Minor Changes

• Added Vargas_18 and Vargas_45 signatures (doi: 10.1371/journal.pcbi.1010770)

TBSignatureProfiler 1.12.0

Bug Fixes

• Removed pROC argument from TableAUC() as it was causing a bug where the upper CI was always the same as the AUC point estimate, even with pROC=FALSE as the default setting.
• Changed source package for rowSums() and rowMeans() to base from BiocGenerics due to an error on the Bioconductor testing servers.

Minor Changes

• Added Chen_5 signature

TBSignatureProfiler 1.10.0

Bug Fixes

• Fixed the tableAUC bootstrapped confidence interval to be the 2.5 and 97.5 percentiles instead of the 5 and 95 percentiles
• Fixed the upper CI value for the pROC/DeLong AUC CI method in the bootstrapAUC function

Major Changes

• Changed tableAUC confidence interval default to bootstrapped instead of DeLong (pROC argument)

Minor Changes

• Updated the github and website introductions.
• Added Natarajan_7, Kaul_3 signatures
• Added Francisco_OD_2, Kwan_186 signatures
• Shortened some example run times

TBSignatureProfiler 1.8.0

Bug Fixes

• Fixed gene in RESPONSE5 (PNN to RP11-295G20.2) in TBsignatures and TBcommon objects. (Stanley M. Kimbung)
• Fixed a bug in the singscore algorithm called from runTBsigProfiler() that would not allow for the scoring of user-provided signatures.
• Fixed the TB_hiv data to remove unnecessary factor level of Disease metadata.
• Fixed the row numbers of existing sigAnnotData and common_sigAnnotData objects, and added code to update them after new signatures are added.

Major Changes

• If any signatures in the object used with runTBsigProfiler() have <2 genes present in the given sample, the signatures will not be scored. This may affect existing scripts.

Minor Changes

• Reorganized code for OriginalModel.R for clarity.
• Added 4 new signatures (Tabone_OD_11/TB12, Tabone_RES_25/EarlyRESP-TB25, Tabone_RES_27/TREAT-TB27, Long_RES_10)
• Updated the website interface
• Changed HGNChelper installation to be checked during profiling if update_genes = TRUE
• Reorganized code in mkAssay() for clarity. The output_name argument is now appended to all output assays, whereas previously it was only appended to the log of the input assay.

TBSignatureProfiler 1.6.0

Bug Fixes

• Fixed some package tests for the profile.R, OriginalModel.R scripts to increase coverage

Major Changes

• Added the gene_update parameter to runTBsigProfiler() to allow users to check signature/sample gene names for excel mogrified or outdated gene symbols
• Updated gene symbols for original models functions
• Added Chendi_HIV_2 signature (8/24)
• Removed Mendelsoh_RISK_11 as it was originally published in Darboe_RISK_11. Changed Darboe_RISK_11 to RISK11 in common objects. (Thomas Scriba)

Minor Changes

• Rewrote runTBsigProfiler() to be shorter and easier to maintain

TBSignatureProfiler 1.5.0

• 68 signatures currently available

Bug Fixes

• Fixed incorrect names of signatures in Tbcommon and common_sigAnnotData objects

Major Changes

• Added Zimmer_RES_3, Gong_OD_4, Bloom_RES_268, and Bloom_RES_558
• Added Sivakumaran_11 and Mendelsoh_RISK_11 signatures
• Added Estevez_133, Estevez_259, LauxdaCosta_OD_3, and Maertzdorf_15 signatures to the package
• Added Chen_HIV_4, Gliddon_HIV_3, Gliddon_2_OD_4, Kulkarni_HIV_2, and Heycken_FAIL_22 signatures
• Added a COVIDsignatures object to the package that can be used to profile COVID-19 gene transcript signatures, thanks to collaborator Dylan Sheerin (WEHI)
• Added functions to evaluate some signatures using their original models from Johnson lab member Xutao Wang

Minor Changes

• Added mention of COVIDsignatures object to main vignette and website
• Included the OG models tutorial on website (Xutao Wang)
• Added addTBsignature() to more easily facilitate updating signatures in package
• Added pROC option to obtain confidence intervals on AUC values as part of \code{tableAUC()}
• Added citation for newly published paper

compbiomed/TBSignatureProfiler documentation built on May 10, 2024, 8:46 p.m.